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Ran 03 Nov 2017 08:55PM UTC

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Committed 03 Nov 2017 08:18PM UTC coverage: 67.234% (-0.2%) from 67.455%

Job # PERFORM_TESTING=true

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push

travis-ci

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web-flow

Commit Message

Change thread defaults throughout (#712)

The CLI should default to fully utilize available resources, and threads should be limited in only three scenarios:
 - snakemake parallel execution on a single machine
 - shared HPC cluster execution (also snakemake)
 - unit tests when py.test xdist is enabled

In all other scenarios (cloud executions, local workstation executions, single command invocations), we should default to use all cores. This is one area where CLI defaults should differ from snakemake defaults.

This PR:
 - converts all CLI argparse parameters to default threads=`util.misc.available_cpu_count` (snakemake defaults unchanged)
 - ensures that argparse options are `type=int`
 - ensures that unit tests are always setting it to `_CPU`
 - converts some `--numThreads` argparse options to `--threads` for consistency
 - fixes some erroneous situations where `--threads` was offered, but not actually passed downstream
 - and has some topically unrelated optimizations to the Travis build for sphinx documentation

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